Okay, this is all IMO, and should be treated as such. Feel free to disagree with me, I promise not to get offended. Also, please correct any factual errors I may have, I'd appreciate it.
From what I've learned, and from my experience in dealing with these things, "separation of church and state" does not mean a complete and utter lack of religion. Rather, it means that there's no state-sponsored religion, as there were in many countries at the time of the USA's founding. The country may well push the concept of having a religion as a good idea, and I think they do, but they tend not to force the issue. (Except of course for some of W's actions, such as "Jesus Day.") I don't think the state should force religion on those who don't want it, either.
But let's be honest "One nation, under the deity or deities of your choice, if you so choose to have one, but if you don't that's quite alright by us, indivisible, with liberty and justice for all," sounds a bit unwieldy to me. Also, try teaching it to five-year-olds. :-)
How should we settle this? Maybe make the "Under God" part optional, or let people insert whatever deity's name they feel is appropriate, kind of like different pledges that require you to state your name. It'll sound a little garbled, but it's a start. Besides, depending on how garbled it gets, you'll know what kinds of religious discussions to expect...
"One nation, under godgoddessallahbuddhavishnuzeusjupitercthulubob..."
If you don't want to say it, don't, if you do, do. Just don't get bent out of shape if someone takes the opposite opinion.
Now, if you don't mind, I'm going to have some caffeine.